QC Report


general
Report generated at2022-10-07 11:19:54
TitleCTCF_DLPFC-NEUN
DescriptionChIP-seq for CTCF_DLPFC-NEUN
Pipeline versionv1.3.6
Pipeline typetf
Genomehg38
Alignerbowtie2
Sequencing endedness{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}}
Peak callerspp

Alignment quality metrics


SAMstat (raw unfiltered BAM)

rep1rep2ctl1ctl2
Total Reads30549350371961744000000040000000
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads28505603348411803921407039313505
Mapped Reads (QC-failed)0000
% Mapped Reads93.3000000000000193.798.098.3
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Marking duplicates (filtered BAM)

rep1rep2ctl1ctl2
Unpaired Reads26088245315812093382278733714807
Paired Reads0000
Unmapped Reads0000
Unpaired Duplicate Reads35874854098863707783840491
Paired Duplicate Reads0000
Paired Optical Duplicate Reads0000
% Duplicate Reads13.751312.9787999999999982.09262.4929

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1ctl2
Total Reads22500760274823463311500432874316
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads22500760274823463311500432874316
Mapped Reads (QC-failed)0000
% Mapped Reads100.0100.0100.0100.0
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Filtered and duplicates removed


Sequence quality metrics (filtered/deduped BAM)

rep1
rep1
rep2
rep2

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.


Library complexity quality metrics


Library complexity (filtered non-mito BAM)

rep1rep2ctl1ctl2
Total Fragments26083750315753143381050133706952
Distinct Fragments22802267278164963322705432984366
Positions with Two Read24960152886229564878694191
NRF = Distinct/Total0.8741940.8809570.9827440.978563
PBC1 = OneRead/Distinct0.8746950.8818630.9827420.978557
PBC2 = OneRead/TwoRead7.9907448.49909657.80647546.495964

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline


NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Replication quality metrics


IDR (Irreproducible Discovery Rate) plots

rep1_vs_rep2
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
pooled-pr1_vs_pooled-pr2

Reproducibility QC and peak detection statistics

overlapidr
Nt14013040874
N114428842042
N28633733325
Np14760742045
N optimal14760742045
N conservative14013040874
Optimal Setpooled-pr1_vs_pooled-pr2pooled-pr1_vs_pooled-pr2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.05335759651751951.0286490189362432
Self Consistency Ratio1.67121859689356821.2615753938484622
Reproducibility Testpasspass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks299998299998

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size268.090.0174.0174.0
25 percentile1070.0360.0394.0696.0
50 percentile (median)1070.0360.0474.0696.0
75 percentile1070.0360.0696.0696.0
Max size1457.0722.01249.01249.0
Mean1015.3389655931039351.7835452236348499.2478772743489635.3223559858272

rep1
rep1
rep2
rep2
idr_opt
idr_opt
overlap_opt
overlap_opt

Enrichment / Signal-to-noise ratio


Strand cross-correlation measures (trimmed/filtered SE BAM)

rep1rep2
Number of Subsampled Reads1500000015000000
Estimated Fragment Length775110
Cross-correlation at Estimated Fragment Length0.1438443482794740.240939341359956
Phantom Peak105105
Cross-correlation at Phantom Peak0.25616650.2407954
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.13818780.1427779
NSC (Normalized Strand Cross-correlation coeff.)1.0409341.687511
RSC (Relative Strand Cross-correlation coeff.)0.047945611.001469


Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.


rep1
rep1
rep2
rep2

Jensen-Shannon distance (filtered/deduped BAM)

rep1rep2
AUC0.214096341532902220.24995418553945006
Synthetic AUC0.492493219880167530.49320529279160485
X-intercept0.152643682758069030.11963764348278207
Synthetic X-intercept1.247920009308443e-1512.192223668013554e-185
Elbow Point0.6879494460664720.647798264208295
Synthetic Elbow Point0.50695183522276850.5077666479734748
JS Distance0.254607013423690460.2043369475000046
Synthetic JS Distance0.381144000378673130.33462691605160017
% Genome Enriched22.24153101627804625.18597768267808
Diff. Enrichment33.9193113751032227.463248605819658
CHANCE Divergence0.293248043049029850.2362409545041476

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.2842638648650090.227920680425171860.29013295550905840.238418292237496750.29062991650059820.238718193854338350.270707706719946540.2733441975374640.27338785228753093

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.200073060685744490.192632648852749860.147678476939341360.20344473990872036

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.12883479069908140.105328531125170880.109585186068176270.13107900897555266

For spp raw peaks:


For overlap/IDR peaks: